hexrd: macros.xml annotate

annotate macros.xml @ 10:a35bda7ed678 draft default tip

"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty"

author	ximgchess
date	Thu, 07 Jul 2022 01:53:44 +0000
parents	e67ad9795525
children

rev	line source
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	1 <macros>
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	2 <token name="@TOOL_VERSION@">0.8.19</token>
8 4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty" ximgchess parents: 7 diff changeset	3 <token name="@VERSION_SUFFIX@">0</token>
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	4 <token name="@PROFILE@">22.01</token>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	5 <xml name="requirements">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	6 <requirements>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	8 <yield/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	9 </requirements>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	10 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	11 <xml name="citations">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	12 <citations>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	13 <citation type="doi">10.1016/j.matchar.2020.110366</citation>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	14 <yield />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	15 </citations>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	16 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	17
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	18 <token name="@CMD_IMPORTS@">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	19 #import re
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	20 #import yaml
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	21
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	22 #set global $img_panel_dict = dict()
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	23 #if $detector.panel_assignment == 'panel_table'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	24 #set $fh = open(str($detector.image_panel_table),'r')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	25 #for $line in $fh:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	26 #set $fields = $line.strip().split('\t')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	27 #silent $img_panel_dict[$fields[0]] = $fields[1]
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	28 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	29 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	30 #set global $panels = $yaml.safe_load(open(str($instrument),'r'))['detectors'].keys()
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	31 #def identifier_or_name($input1)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	32 #if hasattr($input1, 'element_identifier')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	33 #return $input1.element_identifier
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	34 #elif hasattr($input1, 'name')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	35 #return $input1.name
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	36 #else
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	37 #return str($input1)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	38 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	39 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	40 #def clean($name1)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	41 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](npz\|hexrd\|yml\|dat\|out)$','', $name1.split()[-1]))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	42 #return $name_clean
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	43 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	44 #def ln_name($ds,$ext)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	45 #set $lname = "%s.%s" % ($clean($identifier_or_name($ds)),$ext)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	46 #return $lname
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	47 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	48 #def get_panel($img_input):
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	49 #set $img_name = $identifier_or_name($img_input)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	50 #if $img_panel_dict and $img_name in $img_panel_dict:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	51 #return $img_panel_dict[$img_name]
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	52 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	53 #for $p in $panels:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	54 #if $p in $img_name:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	55 #return $p
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	56 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	57 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	58 #return $img_name
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	59 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	60 </token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	61
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	62 <xml name="common_config" token_multiple_inputs="true" >
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	63 <param name="analysis_name" type="text" value="analysis" label="analysis name">
a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	64 <validator type="empty_field" />
a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	65 </param>
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	66 <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	67 <conditional name="detector">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	68 <param name="panel_assignment" type="select" label="Assign detector panel to images">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	69 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	70 <option value="panel_table">Input a table with image panels assignments</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	71 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	72 <when value="infer_from_name"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	73 <when value="panel_table">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	74 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	75 <help>A 2-column table:image dataset name detector panel name</help>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	76 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	77 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	78 </conditional>
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	79 <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	80 <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	81 <param name="active_material" type="select" label="active material name">
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	82 <options>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	83 <filter type="data_meta" ref="material" key="materials"/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	84 </options>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	85 </param>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	86 <param name="dmin" type="float" value="1.0" min="0" max="10" optional="true" label="dmin angstroms" help="used to figure out the maximum sampling for g-vectors default 1.0"/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	87 <param name="tth_width" type="float" value="0.25" min="0" max="10" optional="true" label="tth tolerance in degrees" help="tth_width default 0.25 "/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	88 <param name="min_sfac_ratio" type="float" value="" min="0" max="1" optional="true" label="min percentage of max to exclude" help="min_sfac_ratio min percentage of max \|F\|^2 to exclude; default None"/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	89 <!--
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	90 <param name="active_material" type="text" value="" label="active material name">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	91 <validator type="empty_field" />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	92 </param>
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	93 -->
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	94 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	95
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	96 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	97 mkdir -p imageseries &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	98 ln -s '$material' $ln_name($material,'h5') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	99 ln -s '$instrument' $ln_name($instrument,'yml') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	100 #for $input in $inputs
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	101 ln -s '$input' imageseries/$ln_name($input,'npz') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	102 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	103 ]]>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	104 </token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	105 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	106 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	107 ## hexrd looks for file named: accepted_orientations_{analysis_id}_{active_material}.dat
a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	108 #set $accepted_orientations_name = 'accepted_orientations_analysis_' + str($active_material) + '.dat'
a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	109 ln -s '$accepted_orientations' '$accepted_orientations_name' &&
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	110 ##mkdir -p analysis &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	111 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	112 ]]>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	113 </token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	114
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	115 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs].out'`; do sed -i.bak "s/[ ][ ][ ]/\$(printf '\t')/g" \${i}; done]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	116
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	117 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	118 #slurp
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	119 #set instrument_file = $ln_name($instrument,'yml')
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	120 analysis_name: analysis
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	121
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	122 multiprocessing: -1
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	123
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	124 material:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	125 definitions: $ln_name($material,'h5')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	126 active: $active_material
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	127 #if $dmin
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	128 dmin: $dmin # defaults to 1.0 angstrom
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	129 #end if
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	130 #if $tth_width
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	131 tth_width: $tth_width # defaults to 0.25 degrees
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	132 #end if
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	133 #if $min_sfac_ratio
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	134 min_sfac_ratio: $min_sfac_ratio # min percentage of max \|F\|^2 to exclude; default None
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	135 #end if
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	136
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	137 image_series:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	138 format: frame-cache
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	139 data:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	140 #for $input in $inputs
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	141 - file: imageseries/$ln_name($input,'npz')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	142 args: {}
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	143 panel: $get_panel($input) # must match detector key
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	144 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	145
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	146 instrument: $instrument_file
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	147
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	148 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	149
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	150 <xml name="find_orientations_config">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	151 <expand macro="common_config" token_multiple_inputs="true" />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	152 <section name="orientation_maps" title="Orientation Maps" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	153 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	154 <param name="bin_frames" type="integer" value="1" label="bin frames"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	155 <!-- active_hkls should be able to be optional="true" -->
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	156 <param name="active_hkls" type="text" value="" label="active hkl planes">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	157 <help>commas separated list of planes, e.g.: 0,1,2,3,4,5</help>
8 4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty" ximgchess parents: 7 diff changeset	158 <validator type="regex" message="plane indices separated by commas">^\d(,\d)*$</validator>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	159 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	160 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	161 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	162 <section name="search_options" title="Search Options" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	163 <conditional name="search">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	164 <param name="search_type" type="select" label="Specify Search">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	165 <option value="seed_search" selected="true">use seed search</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	166 <option value="use_quaternion_grid">use quaternion grid</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	167 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	168 <when value="seed_search">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	169 <!-- hkl_seeds should be able to be optional="true" -->
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	170 <param name="hkl_seeds" type="text" value="" label="hkl seeds">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	171 <help>commas separated list of planes, e.g.: 0,1,2 (subset of active hkl planes)</help>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	172 <validator type="regex" message="">^\d(,\d)*$</validator>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	173 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	174 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	175 <conditional name="params">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	176 <param name="method" type="select" label="Method">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	177 <option value="label" selected="true">label</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	178 <option value="blob_dog">blob_dog</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	179 <option value="blob_log">blob_log</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	180 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	181 <when value="label">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	182 <param name="filter_radius" type="integer" value="1" min="1" label="label filter radius"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	183 <param name="threshold" type="integer" value="1" min="1" label="label threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	184 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	185 <when value="blob_dog">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	186 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_dog min_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	187 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_dog max_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	188 <param name="sigma_ratio" type="float" value="1.6" min="0" max="10" label="blob_dog sigma_ratio"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	189 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_dog threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	190 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_dog overlap"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	191 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	192 <when value="blob_log">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	193 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_log min_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	194 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_log max_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	195 <param name="num_sigma" type="integer" value="10" min="0" max="20" label="blob_log num_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	196 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_log threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	197 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_log overlap"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	198 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	199 </conditional>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	200 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	201 <when value="use_quaternion_grid">
7 baba452d0613 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c6c9ce811a27cdee735c2eeac9f6a29f95d9ae90" ximgchess parents: 6 diff changeset	202 <param name="quaternion_grid" type="data" format="npz" label="quaterion grid file"/>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	203 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	204 </conditional>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	205 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	206 <section name="omega" title="Omega" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	207 <param name="omega_tolerance" type="float" value="1.0" min="0" max="10.0" label="omega tolerance"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	208 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	209 <section name="eta" title="eta" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	210 <param name="eta_tolerance" type="float" value="1.0" min="0" max="10.0" label="eta tolerance"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	211 <param name="eta_mask" type="float" value="5.0" min="0" max="10.0" label="eta mask"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	212 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	213 <section name="clustering" title="Clustering" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	214 <param name="clustering_algorithm" type="select" label="Clustering algorithm">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	215 <option value="dbscan" selected="true">dbscan</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	216 <option value="sph-dbscan">sph-dbscan</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	217 <option value="ort-dbscan">ort-dbscan</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	218 <option value="fclusterdata">fclusterdata (won't work for large problems)</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	219 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	220 <param name="clustering_radius" type="float" value="1.0" min="0" max="10" label="clustering radius"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	221 <param name="clustering_completeness" type="float" value="0.85" min="0" max="1" label="clustering completeness threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	222 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	223 <!--
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	224 -->
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	225 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	226
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	227 <token name="@FIND_ORIENTATIONS_YML@"><![CDATA[@COMMON_YML@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	228
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	229 #set active_hkls = 'all'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	230 #if $orientation_maps.active_hkls:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	231 #set active_hkls = '[' + str($orientation_maps.active_hkls) + ']'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	232 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	233 find_orientations:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	234 orientation_maps:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	235 # A file name must be specified. If it doesn't exist, one will be created
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	236 file: null
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	237
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	238 threshold: $orientation_maps.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	239 bin_frames: $orientation_maps.bin_frames # defaults to 1
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	240
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	241 # "all", or a list of hkl orders used to find orientations
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	242 # defaults to all orders listed in the material definition
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	243 active_hkls: $active_hkls
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	244
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	245 # either search full quaternion grid, or seed search based on sparse
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	246 # orientation maps. For input search space:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	247 #
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	248 # use_quaternion_grid: some/file/name
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	249 #
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	250 # otherwise defaults to seeded search
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	251 #if $search_options.search.search_type == 'use_quaternion_grid'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	252 use_quaternion_grid:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	253 #elif $search_options.search.search_type == 'seed_search'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	254 #set hkl_seeds = '[' + str($search_options.search.hkl_seeds) + ']'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	255 seed_search: # this section is ignored if use_quaternion_grid is defined
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	256 hkl_seeds: $hkl_seeds # hkls ids to use, must be defined for seeded search
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	257 fiber_step: $search_options.search.fiber_step # degrees, defaults to ome tolerance
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	258 # Method selection:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	259 # Now 3 choices: label (the original), 'blob_dog', and 'blob_log'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	260 # Each has its own parameter names, examples below.
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	261 #
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	262 method:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	263 #if $search_options.search.params.method == 'label'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	264 label:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	265 filter_radius: $search_options.search.params.filter_radius
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	266 threshold: $search_options.search.params.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	267 #elif $search_options.search.params.method == 'blob_dog'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	268 blob_dog:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	269 min_sigma: $search_options.search.params.min_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	270 max_sigma: $search_options.search.params.max_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	271 sigma_ratio: $search_options.search.params.sigma_ratio
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	272 threshold: $search_options.search.params.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	273 overlap: $search_options.search.params.overlap
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	274 #elif $search_options.search.params.method == 'blob_log'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	275 blob_log:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	276 min_sigma: $search_options.search.params.min_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	277 max_sigma: $search_options.search.params.max_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	278 num_sigma: $search_options.search.params.num_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	279 threshold: $search_options.search.params.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	280 overlap: $search_options.search.params.overlap
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	281 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	282 # this is the on-map threshold using in the scoring
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	283 # defaults to 1
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	284 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	285 threshold: $on_map_threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	286
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	287 omega:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	288 tolerance: $omega.omega_tolerance # in degrees, defaults to 2x ome step
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	289
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	290 eta:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	291 tolerance: $eta.eta_tolerance # in degrees, defaults to 2x ome step
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	292 mask: $eta.eta_mask # degrees, mask angles close to ome rotation axis, defaults to 5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	293
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	294 clustering:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	295 # algorithm choices are
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	296 # sph-dbscan
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	297 # ort-dbscn
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	298 # dbscan <default>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	299 # fclusterdata; this is a fallback and won't work for large problems
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	300 algorithm: $clustering.clustering_algorithm
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	301 radius: $clustering.clustering_radius
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	302 completeness: $clustering.clustering_completeness
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	303
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	304 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	305
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	306 <xml name="fit_grains_config">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	307 <expand macro="common_config" token_multiple_inputs="true"/>
6 164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636" ximgchess parents: 5 diff changeset	308 <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	309 <param name="accepted_orientations" type="data" format="hexrd.accepted_orientations" label="accepted_orientations from find_orientations"/>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	310 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	311 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	312 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	313 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	314 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	315 <repeat name="tolerance_lists" title="Tolerance values" min="1">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	316 <param name="tth" type="float" value="" min="0" label="tth"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	317 <param name="eta" type="float" value="" min="0" label="eta"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	318 <param name="omega" type="float" value="" min="0" label="omega"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	319 </repeat>
8 4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty" ximgchess parents: 7 diff changeset	320 <param name="refit" type="text" value="1" label="refit" help="float values separated by commas">
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	321 <validator type="regex" message="">^[+-]?(\d+(\.\d)?\|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d)?\|\.\d+)([eE][+-]?\d+)?)+$</validator>
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	322 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	323 <conditional name="max_tth">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	324 <param name="tth_max_value" type="select" label="Set tth_max">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	325 <option value="true" selected="true">true</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	326 <option value="false">false</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	327 <option value="entered">enter value</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	328 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	329 <when value="true"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	330 <when value="false"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	331 <when value="entered">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	332 <param name="tth_max" type="float" value="14.25" label="tth_max"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	333 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	334 </conditional>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	335 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	336 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	337
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	338 <token name="@FIT_GRAINS_YML@"><![CDATA[@COMMON_YML@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	339 find_orientations:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	340 orientation_maps:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	341 # A file name must be specified. If it doesn't exist, one will be created
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	342 file: $ln_name($ome_map,'npz')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	343
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	344 fit_grains:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	345 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	346 # estimate: null
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	347 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	348 threshold: $threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	349
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	350 #set $tth = []
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	351 #set $eta = []
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	352 #set $omega = []
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	353 ## #set $refit_tol = str($tolerance.refit)
a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	354 ## #set $refit = '[' + $refit_tol + ']'
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	355 #for $tol in $tolerance.tolerance_lists
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	356 #silent $tth.append(float($tol.tth))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	357 #silent $eta.append(float($tol.eta))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	358 #silent $omega.append(float($tol.omega))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	359 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	360 tolerance:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	361 tth: $tth # tolerance lists must be identical length
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	362 eta: $eta
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	363 omega: $omega
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	364
10 a35bda7ed678 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty" ximgchess parents: 9 diff changeset	365 refit: [${tolerance.refit}]
5 36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	366 #if $tolerance.max_tth.tth_max_value == 'entered':
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	367 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	368 #else
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	369 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	370 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	371 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	372 <token name="@HEXRD_HELP@"><![CDATA[
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	373 HEXRD_ provides analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	374
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	375 .. _HEXRD: https://github.com/HEXRD/hexrd
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	376 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	377
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	378 <token name="@COMMON_INPUTS_HELP@"><![CDATA[
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	379
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	380 INPUTS
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	381
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	382 - imageseries - Detector image files converted to sparse matrix compressed numpy arrays.
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	383 - instrument - A yaml file that decribes the instrument
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	384 - materials.hexrd - A "pickled" hexrd Materials object that desscribes the sample material
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	385 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	386 <token name="@FIT_GRAIN_INPUTS_HELP@"><![CDATA[@COMMON_INPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	387 - analysis eta-ome_maps.npz from find_orientations
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	388 - accepted_orientations from find_orientations
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	389
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	390 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	391
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	392 <token name="@COMMON_OUTPUTS_HELP@"><![CDATA[
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	393
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	394 OUTPUTS
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	395
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	396 - config yaml - parameter for hexrd
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	397 - log - the hexrd logging output
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	398 - grains.out
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	399 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	400 <token name="@FIND_ORIENTATIONS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	401 - analysis eta-ome_maps.npz (used as input for hexrd fit-grains)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	402 - analysis accepted_orientations_analysis.dat (used as input for hexrd fit-grains)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	403 - analysis scored_orientations_analysis.npz
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	404 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	405 <token name="@FIT_GRAINS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	406 - Collection of spots.out
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	407 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	408
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	409
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" ximgchess parents: diff changeset	410 </macros>

Mercurial > repos > ximgchess > hexrd

annotate macros.xml @ 10:a35bda7ed678 draft default tip